The disavow tool is primarily for 3rd party consultants working on Manual Reviews that don't have historical knowledge of the website, the customers self developed link schemes, satellite sites, past promotional developments, etc. that they don't recall they did or don't wish to admit to.

If the owner provides all correspondence, emails, receipt for all transactional links you can quickly remove these from the profile... but how long does it take to review any link and determine it is LIKELY violating Google guidelines? Hindsight is needed for recovery from a Manual Review.

Adding original content to your domain isn't going to get you into trouble but how often does anyone simply add content to their own domain for link development?

One traded link isn't going to get you into trouble... but 5000 most certainly will

One directory link isn't going to get you into trouble... but 5000 most certainly will

One article link isn't going to get you into trouble... but 5000 most certainly will

One comment link on a blog isn't going to get you into trouble... but 5000 most certainly will

One paid link that doesn't have rel="nofollow" in the link element isn't going to get you into trouble... but 5000 most certainly will

One three-way or four-way link isn't going to get you into trouble... but 5000 most certainly will

So you can see a pattern between what won't cause you problems and what will but where is the threshold that something that starts as being OK becomes a scheme? Additionally, when you start profile building through multiple versions of the previously noted schemes - the complexity of the devaluation grows exponientially.

A site's owner's lack of knowledge of their our scheming practices will hamper a consultants ability to aid recovery because what the site owner did 10 years ago can be the cause of the devaluation. Just because the site owner got away with it for 10 years does not mean they weren't violating Google's guidelines for 10 years.

How much time does it take to evaluate a single link where you have zero knowledge on how it was developed?

The larger the profile the larger the problem and that generally means the greater the cost as time is money so Google leveled the playing field with the Disavow tool.

That said, PENGUIN does the precise same thing that the disavow tool does... both disavow links so they have no impact on results. You cannot use the Disavow Tool to UNDO PENGUIN you can only use it to demonstrate to Googlebot... "DO NOT INCLUDE IN THE LINK GRAPH"... which is generally why you lost ranks in the first place.